6SXR image
Deposition Date 2019-09-26
Release Date 2020-02-26
Last Version Date 2024-10-23
Entry Detail
PDB ID:
6SXR
Keywords:
Title:
E221Q mutant of GH54 a-l-arabinofuranosidase soaked with 4-nitrophenyl a-l-arabinofuranoside
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.64 Å
R-Value Free:
0.18
R-Value Work:
0.15
Space Group:
H 3 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Alpha-L-arabinofuranosidase B
Gene (Uniprot):abfB
Chain IDs:A
Chain Length:482
Number of Molecules:1
Biological Source:Aspergillus kawachii IFO 4308
Primary Citation
Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-l-Arabinofuranosidases.
J.Am.Chem.Soc. 142 4648 4662 (2020)
PMID: 32053363 DOI: 10.1021/jacs.9b11351

Abstact

Identifying and characterizing the enzymes responsible for an observed activity within a complex eukaryotic catabolic system remains one of the most significant challenges in the study of biomass-degrading systems. The debranching of both complex hemicellulosic and pectinaceous polysaccharides requires the production of α-l-arabinofuranosidases among a wide variety of coexpressed carbohydrate-active enzymes. To selectively detect and identify α-l-arabinofuranosidases produced by fungi grown on complex biomass, potential covalent inhibitors and probes which mimic α-l-arabinofuranosides were sought. The conformational free energy landscapes of free α-l-arabinofuranose and several rationally designed covalent α-l-arabinofuranosidase inhibitors were analyzed. A synthetic route to these inhibitors was subsequently developed based on a key Wittig-Still rearrangement. Through a combination of kinetic measurements, intact mass spectrometry, and structural experiments, the designed inhibitors were shown to efficiently label the catalytic nucleophiles of retaining GH51 and GH54 α-l-arabinofuranosidases. Activity-based probes elaborated from an inhibitor with an aziridine warhead were applied to the identification and characterization of α-l-arabinofuranosidases within the secretome of A. niger grown on arabinan. This method was extended to the detection and identification of α-l-arabinofuranosidases produced by eight biomass-degrading basidiomycete fungi grown on complex biomass. The broad applicability of the cyclophellitol-derived activity-based probes and inhibitors presented here make them a valuable new tool in the characterization of complex eukaryotic carbohydrate-degrading systems and in the high-throughput discovery of α-l-arabinofuranosidases.

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